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Will it make a difference in running speed if we run samples of same no of bases but different AT - GC content ?

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Can we get a little more information on the DNA? Is it linear, cut, or nicked? Is it an uncut plasmid or chromosome? In cut linear DNA I don't think you would see a difference, but you could certainly see differences in the migration of the super-coil. –  Atl LED Nov 14 '13 at 20:40
    
@AtlLED why? Are you thinking about mechanical things like long stretches of As that will make it bend or something else? –  terdon Nov 15 '13 at 0:07
    
Nucleotide does affect the persistent length of the DNA.. but it is not just the length I guess; it is also affected by the sequence pattern. –  WYSIWYG Nov 15 '13 at 6:21
    
@AtlLED It is linear double stranded dna. –  biogirl Nov 15 '13 at 7:37

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It does make a difference on polyacrylamide. A and C are faster while G and T are slower.

Image from publication:

enter image description here

The "standards" are AAA/TTT/GGG/CCC molecules.

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nice find - i think that proves the point! –  shigeta Apr 9 at 3:37

Practically speaking I have never seen a difference, but the agarose gels usually used in the lab do not have the highest resolution. There is one paper showing that the form (A- or B- form) and the GC-content play a role since DNA molecules of higher GC content are less flexible and therefore have more problems getting through the agarose matrix. Interesting paper, but probably not very relevant in the lab (under "related publications" on the right side of the PubMed site you can find more on this topic):

There is however a technique, which makes use of the different GC content of DNA samples. It is called "Denaturing Gradient Gel Electrophoresis" and makes use of gradients (either chemical or temperature) to denaturate DNA on the gel. Depending on the GC content, this happens earlier or later, which influences the migration pattern (denaturated DNA is much bigger and slower). See here for more details.

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if you run a circular plasmid on an agarose gel you can see more than one band due to different ways the plasmid dna can twist. In extreme circumstances I could see it making a difference. Usually it would not. –  shigeta Apr 8 at 19:14
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Ok, I was assuming we compare doublestranded DNA of approximately the same size with different base compositions. In the case of the plasmid the different shapes (coiled, supercoiled, relaxed) make the difference. –  Chris Apr 8 at 19:38
    
hey Chris I was just supporting what you were saying - that if you had an odd collection of bases it might bend up like a supercoiled plasmid and would be visible on a gel. –  shigeta Apr 9 at 3:37

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